\ProvidesPackage{hithesis}[2018/02/19 1.0.10 Harbin Institute of Technology
Thesis Template Extension]
% 此文件声明不在规范中要求的格式所使用的宏包。
% （所以，格式基本上是自由发挥的。）

% 根据窝工规范中对数字书写规范的规定（6）：
% 凡4位或4位以上的数都从个位起每3位数空半个数码(1/4汉字)。
% 注意此处，除此任何空格都是错误的（包括\:\;\ 等）
\RequirePackage{siunitx}
\sisetup{group-minimum-digits=4, group-separator= \hspace{0.25em}}

% 处理数学公式中的黑斜体的宏包
\RequirePackage{bm}
% 不同于 \mathcal \mathfrak 之类的英文花体字体
\RequirePackage{mathrsfs}
% 支持彩色
\RequirePackage{xcolor}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%  set global color theme of thesis  %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\definecolor{colorzero}{rgb}{0, 0, 0}
\definecolor{colorone}{rgb}{1, 0, 0}
\definecolor{colortwo}{rgb}{0, 0, 1}
\definecolor{colorthree}{rgb}{0, 1, 0}
% 图形和表格的控制旋转
\RequirePackage{rotating}



% 算法的宏包，注意宏包兼容性，先后顺序为float、hyperref、algorithm(2e)，否则无法
% 生成算法列表。我工算法混乱问题详见hithesis文档。各个实验室设置具体方法详见
% hithesis文档或者示例中给出的地址。
\RequirePackage[boxed,linesnumbered,algochapter]{algorithm2e}
\newcommand{\algoenname}{Algo.} %算法英文标题
\newfloatlist[chapter]{algoen}{aen}{\listalgoenname}{\algoenname}
\newfixedcaption{\algoencaption}{algoen}
\renewcommand{\thealgoen}{\thechapter-\arabic{algocf}}
\renewcommand{\@cftmakeaentitle}{\chapter*{\listalgoenname\@mkboth{\bfseries\listalgoenname}{\bfseries\listalgoenname}}
}
\renewcommand{\algorithmcfname}{算法}
\setlength\AlCapSkip{1.2ex}
\SetAlgoSkip{1pt}
\renewcommand{\algocf@captiontext}[2]{\wuhao#1\algocf@typo ~ \AlCapFnt{}#2} % text of caption
\expandafter\ifx\csname algocf@within\endcsname\relax% if \algocf@within doesn't exist
\renewcommand\thealgocf{\@arabic\c@algocf} % and the way it is printed
\else%                                    else
\renewcommand\thealgocf{\csname the\algocf@within\endcsname-\@arabic\c@algocf}
\fi
\renewcommand{\algocf@makecaption}[2]{%中英文双标题一定多于一行，因此去掉单行时的判断，并将\parbox中标题设置为居中
  \addtolength{\hsize}{\algomargin}%
  \sbox\@tempboxa{\algocf@captiontext{#1}{#2}}%
    \hskip .5\algomargin%
    \parbox[t]{\hsize}{\centering\algocf@captiontext{#1}{#2}}%
  \addtolength{\hsize}{-\algomargin}%
}
\newcommand{\AlgoBiCaption}[2]{%直接取出自定义的中英文标题条目加入到真正的\caption 中
   \caption[#1]{\protect\setlength{\baselineskip}{1.5em}#1 \protect \\ Algo. \thealgocf~~ #2} % \algoencaption{#2}
   \addcontentsline{aen}{algoen}{\protect\numberline{\thealgoen}{#2}}
}

% 排版源码所使用的环境可以有两种。listings和minted
\RequirePackage{listings}
\lstset{
% basicstyle=\small\ttfamily,
columns=flexible,
breaklines=true
}

% 或者使用minted 包。如果使用该包，需要在编译时加-shell-escape选项，且需要安装
% pygmentatize 工具对代码进行高亮。
% \RequirePackage{minted}
%

% 术语宏包，用来处理首次全写，之后缩写的问题
\RequirePackage{glossaries}
\setacronymstyle{short-long}
\renewcommand*{\genacrfullformat}[2]{%
   \glsentrylong{#1}%
}
\makeglossaries
% 添加术语举例

\newacronym{tssbp}{树结构折筷过程}{树结构折筷过程（Tree-structured Stick-breaking process）}
\def\gtssbp{\gls{tssbp}\sindex[china]{shu!树结构折筷过程}\sindex[english]{Tree-structured Stick-breaking process}}

\newacronym[shortplural=SCNAs,longplural={体细胞拷贝数变异（Somatic copy number alternation，SCNA）}]{scna}{SCNA}{体细胞拷贝数变异（Somatic copy number alternation，SCNA）}
\def\gscna{\gls{scna}\sindex[china]{ti!体细胞拷贝数变异}\sindex[english]{Somatic copy number alternation}\ignorespaces}
\def\gscnas{\glspl{scna}\sindex[china]{ti!体细胞拷贝数变异}\sindex[english]{Somatic copy number alternation}\ignorespaces}

% tikz做图宏宏包
\usepackage{tikz}
% 此处可以定义一些tikz全局样式
% \tikzstyle{nodestyle}= [circle, fill=gray!60]
% \tikzstyle{edgestyle}= [-latex]

\tikzstyle{maternal}= [colorone]
\tikzstyle{paternal}= [colortwo]
\tikzstyle{variant}= [colorthree!80!colorzero]
\tikzstyle{reference}= [colorzero]

\tikzstyle{aallele}= [colorzero,rotate=90]
\tikzstyle{ballele}= [colorthree!80!colorzero,rotate=90]

\tikzstyle{refseg}= [colorzero,draw=colorzero, opacity=0.2]
\tikzstyle{mseg}= [colorone,draw=colorone, opacity=0.2]
\tikzstyle{pseg}= [colortwo,draw=colortwo, opacity=0.2]
\tikzstyle{vseg}= [colorthree!80!colorzero,draw=colorthree!80!colorzero, opacity=0.6]

\tikzstyle{bncell}= [draw=colorzero,opacity=0.2,line width=2pt, rounded corners=1pt]
\tikzstyle{btcell}= [draw=colorone,opacity=0.6, line width=2pt, rounded corners=1pt]

\tikzstyle{tncell}= [colorzero,opacity=0.9]
\tikzstyle{ttcell}= [colorone,opacity=0.6]
\tikzstyle{tscell}= [colorzero]
\tikzstyle{refcell}= [colorzero]

\tikzstyle{evolve}= [->,draw=colortwo,opacity=0.3,line width=1.5pt]
\tikzstyle{fakeevolve}= [->,draw=colorzero,opacity=0.3,line width=1.5pt]

\tikzstyle{refline}= [dashed,draw=colorzero,line width=1pt]
\tikzstyle{tnline}= [dashed,draw=colorzero,opacity=0.3,line width=1pt]

\newcommand{\gseg}[9]{%
	\pgfmathsetmacro{\sstartx}{#1}
	\pgfmathsetmacro{\slengx}{#2}
	\pgfmathsetmacro{\sy}{#3}
	\pgfmathsetmacro{\sdy}{#4}
	\pgfmathsetmacro{\sdx}{#5}
	\pgfmathsetmacro{\sdxh}{#7}
	\pgfmathsetmacro{\sdxt}{#8}
	\fill[#6](\sstartx,\sy)--(\sstartx-\sdx,\sy+\sdy)--
	(\slengx+\sstartx+1.5-\sdx,\sy+\sdy)--(\slengx+\sstartx+1.5,\sy)--
	(\slengx+\sstartx+1.5-\sdx,\sy-\sdy)--(\sstartx-\sdx,\sy-\sdy)--cycle;
	\draw[#9] (\sstartx-\sdxh,\sy) -- (\sstartx, \sy);
	\draw[#9] (\slengx+\sstartx+1.5, \sy) -- (\slengx+\sstartx+1.5+\sdxt,\sy);
}
\newcommand{\gsegr}[9]{%
	\pgfmathsetmacro{\sstartx}{#1}
	\pgfmathsetmacro{\slengx}{#2}
	\pgfmathsetmacro{\sy}{#3}
	\pgfmathsetmacro{\sdy}{#4}
	\pgfmathsetmacro{\sdx}{#5}
	\pgfmathsetmacro{\sdxh}{#7}
	\pgfmathsetmacro{\sdxt}{#8}
	\fill[#6](\sstartx-0.5,\sy)--(\sstartx+\sdx-0.5,\sy+\sdy)--
	(\slengx+\sstartx+1.5+\sdx-0.5,\sy+\sdy)--(\slengx+\sstartx+1.5-0.5,\sy)--
	(\slengx+\sstartx+1.5+\sdx-0.5,\sy-\sdy)--(\sstartx+\sdx-0.5,\sy-\sdy)--cycle;
	\draw[#9] (\sstartx-\sdxh-0.5,\sy) -- (\sstartx-0.5, \sy);
	\draw[#9] (\slengx+\sstartx+1.5-0.5, \sy) -- (\slengx+\sstartx+1.5+\sdxt-0.5,\sy);
}

\newcommand{\rcell}[2]{%
	\pgfmathsetmacro{\x}{#1}
	\pgfmathsetmacro{\y}{#2}
	%\node at (\x+10, \y) {Reference};
	\draw (\x+1,\y) node[aallele]{A};
	\draw (\x+2,\y) node[aallele]{C};
	\draw (\x+3,\y) node[aallele]{T};
	\draw (\x+4,\y) node[aallele]{C};
	\gseg{\x}{4}{\y}{0.2}{0.5}{refseg}{1.5}{1}{reference};
}

\newcommand{\ncell}[2]{%
	\pgfmathsetmacro{\x}{#1}
	\pgfmathsetmacro{\y}{#2}
	%\node [maternal] at (\x+8, \y) {M};
	%\node [paternal] at (\x+8, \y-0.5) {P};
	\draw[bncell](\x-2,\y+0.5)--(\x+7,\y+0.5)--
	(\x+7,\y-1)--(\x-2,\y-1)--cycle;
	\draw (\x+1,\y) node[aallele]{A};
	\draw (\x+2,\y) node[ballele]{G};
	\draw (\x+3,\y) node[aallele]{T};
	\draw (\x+4,\y) node[aallele]{C};
	\gseg{\x}{4}{\y}{0.2}{0.5}{mseg}{1.5}{1}{maternal};
	\draw (\x+1,\y-0.5) node[ballele]{T};
	\draw (\x+2,\y-0.5) node[aallele]{C};
	\draw (\x+3,\y-0.5) node[aallele]{T};
	\draw (\x+4,\y-0.5) node[ballele]{A};
	\gseg{\x}{4}{\y-0.5}{0.2}{0.5}{pseg}{1.5}{1}{paternal};
}

\newcommand{\tcellone}[2]{%
	\pgfmathsetmacro{\x}{#1}
	\pgfmathsetmacro{\y}{#2}
	%\node [maternal] at (\x+8, \y) {M};
	%\node [maternal] at (\x+8, \y-0.5) {M};
	%\node [paternal] at (\x+8, \y-1) {P};
	\draw[btcell](\x-2,\y+0.5)--(\x+7,\y+0.5)--
	(\x+7,\y-1.5)--(\x-2,\y-1.5)--cycle;
	\draw (\x+1,\y) node[aallele]{A};
	\draw (\x+2,\y) node[ballele]{G};
	\draw (\x+3,\y) node[aallele]{T};
	\draw (\x+4,\y) node[aallele]{C};
	\gseg{\x}{4}{\y}{0.2}{0.5}{mseg}{1.5}{1}{maternal};
	\draw (\x+1,\y-0.5) node[aallele]{A};
	\draw (\x+2,\y-0.5) node[ballele]{G};
	\draw (\x+3,\y-0.5) node[aallele]{T};
	\draw (\x+4,\y-0.5) node[aallele]{C};
	\gseg{\x}{4}{\y-0.5}{0.2}{0.5}{mseg}{1.5}{1}{maternal};
	\draw (\x+1,\y-1) node[ballele]{T};
	\draw (\x+2,\y-1) node[aallele]{C};
	\draw (\x+3,\y-1) node[aallele]{T};
	\draw (\x+4,\y-1) node[ballele]{A};
	\gseg{\x}{4}{\y-1}{0.2}{0.5}{pseg}{1.5}{1}{paternal};
}

\newcommand{\tcellthree}[2]{%
	\pgfmathsetmacro{\x}{#1}
	\pgfmathsetmacro{\y}{#2}
	%\node [maternal] at (\x+12, \y) {M};
	%\node [paternal] at (\x+12, \y-0.5) {P};
	\draw[btcell](\x-2,\y+0.5)--(\x+11,\y+0.5)--
	(\x+11,\y-1)--(\x-2,\y-1)--cycle;
	\draw (\x+1,\y) node[aallele]{A};
	\draw (\x+2,\y) node[ballele]{G};
	\gseg{\x}{2}{\y}{0.2}{0.5}{mseg}{1.5}{0}{maternal};
	\gseg{\x+4}{0}{\y}{0.2}{0.5}{vseg}{0.5}{0.5}{variant};
	\draw (\x+7,\y) node[aallele]{T};
	\draw (\x+8,\y) node[aallele]{C};
	\gseg{\x+6}{2}{\y}{0.2}{0.5}{mseg}{0}{1}{maternal};
	\draw (\x+1,\y-0.5) node[ballele]{T};
	\draw (\x+2,\y-0.5) node[aallele]{C};
	\draw (\x+3,\y-0.5) node[aallele]{T};
	\draw (\x+4,\y-0.5) node[ballele]{A};
	\gseg{\x}{4}{\y-0.5}{0.2}{0.5}{pseg}{1.5}{1}{paternal};
}

\newcommand{\tcellfour}[2]{%
	\pgfmathsetmacro{\x}{#1}
	\pgfmathsetmacro{\y}{#2}
	%\node [maternal] at (\x+18, \y) {M};
	%\node [paternal] at (\x+18, \y-0.5) {P};
	\draw[btcell](\x-2,\y+0.5)--(\x+15,\y+0.5)--
	(\x+15,\y-1)--(\x-2,\y-1)--cycle;
	\draw (\x+1,\y) node[aallele]{A};
	\draw (\x+2,\y) node[ballele]{G};
	\gseg{\x}{2}{\y}{0.2}{0.5}{mseg}{1.5}{0}{maternal};
	\gseg{\x+4}{0}{\y}{0.2}{0.5}{vseg}{0.5}{0.5}{variant};
	\draw (\x+7,\y) node[aallele]{T};
	\gseg{\x+6}{1}{\y}{0.2}{0.5}{mseg}{0}{0}{maternal};
	\gseg{\x+9}{0}{\y}{0.2}{0.5}{vseg}{0.5}{0.5}{variant};
	\draw (\x+12,\y) node[aallele]{C};
	\gseg{\x+11}{1}{\y}{0.2}{0.5}{mseg}{0}{1}{maternal};
	\draw (\x+1,\y-0.5) node[ballele]{T};
	\draw (\x+2,\y-0.5) node[aallele]{C};
	\draw (\x+3,\y-0.5) node[aallele]{T};
	\draw (\x+4,\y-0.5) node[ballele]{A};
	\gseg{\x}{4}{\y-0.5}{0.2}{0.5}{pseg}{1.5}{1}{paternal};
}

\newcommand{\tcelltwo}[2]{%
	\pgfmathsetmacro{\x}{#1}
	\pgfmathsetmacro{\y}{#2}
	%\node [maternal] at (\x+8, \y) {M};
	%\node [maternal] at (\x+8, \y-0.5) {M};
	%\node [paternal] at (\x+8, \y-1) {P};
	\draw[btcell](\x-2,\y+0.5)--(\x+7,\y+0.5)--
	(\x+7,\y-1.5)--(\x-2,\y-1.5)--cycle;
	\draw (\x+1,\y)  node[aallele]{A};
	\draw (\x+2,\y)  node[ballele]{G};
	\draw (\x+3,\y)  node[aallele]{T};
	\draw (\x+4,\y)  node[aallele]{C};
	\gseg{\x}{4}{\y}{0.2}{0.5}{mseg}{1.5}{1}{maternal};
	\draw (\x+1,\y-0.5) node[aallele]{A};
	\draw (\x+2,\y-0.5) node[ballele]{G};
	\draw (\x+3,\y-0.5) node[aallele]{T};
	\draw (\x+4,\y-0.5) node[ballele]{G};
	\gseg{\x}{4}{\y-0.5}{0.2}{0.5}{mseg}{1.5}{1}{maternal};
	\draw (\x+1,\y-1) node[ballele]{T};
	\draw (\x+2,\y-1) node[aallele]{C};
	\draw (\x+3,\y-1) node[aallele]{T};
	\draw (\x+4,\y-1) node[ballele]{A};
	\gseg{\x}{4}{\y-1}{0.2}{0.5}{pseg}{1.5}{1}{paternal};
}


\newcommand{\tcellfive}[2]{%
	\pgfmathsetmacro{\x}{#1}
	\pgfmathsetmacro{\y}{#2}
	%\node [maternal] at (\x+8, \y) {M};
	%\node [maternal] at (\x+8, \y-0.5) {M};
	%\node [paternal] at (\x+8, \y-1) {P};
	\draw[btcell](\x-2,\y+0.5)--(\x+9.5,\y+0.5)--
	(\x+9.5,\y-1.5)--(\x-2,\y-1.5)--cycle;
	\draw (\x+1,\y) node[aallele]{A};
	\draw (\x+2,\y) node[ballele]{G};
	\draw (\x+3,\y) node[aallele]{T};
	\draw (\x+4,\y) node[aallele]{C};
	\gseg{\x}{4}{\y}{0.2}{0.5}{mseg}{1.5}{1}{maternal};
	\draw (\x+1,\y-0.5) node[aallele]{A};
	\draw (\x+2,\y-0.5) node[ballele]{G};
	\draw (\x+3,\y-0.5) node[aallele]{T};
	\draw (\x+4,\y-0.5) node[aallele]{C};
	\gseg{\x}{4}{\y-0.5}{0.2}{0.5}{mseg}{1.5}{1}{maternal};
	\draw (\x+1,\y-1) node[ballele]{T};
	\gseg{\x}{1}{\y-1}{0.2}{0.5}{pseg}{1.5}{0}{paternal};
	\draw (\x+4.5,\y-1) node[ballele]{A};
	\draw (\x+5.5,\y-1) node[aallele]{T};
	\draw (\x+6.5,\y-1) node[aallele]{C};
	\gsegr{\x+3.5}{3}{\y-1}{0.2}{0.5}{pseg}{0.5}{1.5}{paternal};
}

% 最后定义一些常见的数学公式样式。格式和内容分离，是LaTeX的巨大优势
% 例如如下定义：
\newcommand{\theVector}[1]{\bm{#1}}
\newcommand{\theMatrix}[1]{\mathbb{#1}}
\newcommand{\theSet}[1]{\mathcal{#1}}
\newcommand{\theDirected}[1]{{\overrightarrow{#1}}}
\newcommand{\theUndirected}[1]{{\overline{#1}}}
\newcommand{\theNetwork}[1]{\mathscr{#1}}
\newcommand{\theNode}[1]{{\text{#1}}}
\newcommand{\theDirectedEdge}[2]{{\overrightarrow{{#1}{#2}}}}
\newcommand{\theUndirectedEdge}[2]{{\overline{{#1}{#2}}}}
% 如果想要修改论文中所有的表示网络的数学符号的样式，不必在正文中处处修改，只需要
% 在这里修改就可以了。

% 定义命令
\def\cmd#1{\cs{\expandafter\cmd@to@cs\string#1}}
\def\cmd@to@cs#1#2{\char\number`#2\relax}
\DeclareRobustCommand\cs[1]{\texttt{\char`\\#1}}
\endinput
